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Full Discussion: Search files in directory for keywords using bash
Top Forums Shell Programming and Scripting Search files in directory for keywords using bash Post 302964162 by sea on Monday 11th of January 2016 04:01:16 PM
Old 01-11-2016
Theoreticly, you could have saved them as CSV (Comma Seperated Values).
However, the IFS here seems to be NL/tab.

Your awk code is invalid.
Code:
1 ~/tmp $ LC_ALL=C sh ccmbade.sh 
awk: cmd. line:1: /chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) ccmbade.dat print > ccmbade.dat_edit.txt
awk: cmd. line:1:                                      ^ syntax error
awk: cmd. line:1: /chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) ccmbade.dat print > ccmbade.dat_edit.txt
awk: cmd. line:1:                                                     ^ syntax error
awk: cmd. line:1: /chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) ccmbade.dat print > ccmbade.dat_edit.txt
awk: cmd. line:1:                                                                    ^ syntax error
awk: cmd. line:1: /chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) ccmbade.dat print > ccmbade.dat_edit.txt
awk: cmd. line:1:                                                                                      ^ syntax error
awk: cmd. line:1: /chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) ccmbade.dat print > ccmbade.dat_edit.txt
awk: cmd. line:1:                                                                                                          ^ syntax error
awk: cmd. line:1: /chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) ccmbade.dat print > ccmbade.dat_edit.txt
awk: cmd. line:1:                                                                                                                       ^ unexpected newline or end of string

Having 3 different kinds of 'columns' doesnt really help.

You know, you dont have to use awk, you could use regular scripting?
If that is easier for you, that is.

This said, counts for me too, here is somethign to get you started:
Code:
for f in *.dat ; do
	bname=${f##*/}
	#pref=${bname%%.bam}	## dont have that
	#awk "/chr/{found=1}/start/{if(found)/stop/{if(found)/ref/{if(found)/alt/{if(found) $f print > ${pref}_edit.txt"
	while read content_line
	do
		if echo "$content_line" | grep -q ^name
		then	
			MODE="default"	# Reset parse mode
			echo "$content_line" | grep -v symbol | grep -q id && MODE=id
			echo "$content_line" | grep -q symbol && MODE=symbol
		fi
		
		case $MODE in
		default)	while read chr start stop ref alt comment;do
					line_print="$chr $start $stop $ref $alt $commet"
				done<<<"$content_line" ##>> ccmcbabe.output
				;;
		id)		echo "id handling"	;;
		symbol)		echo "symbol handling"	;;
		esac
		
		echo "$MODE :: $line_print"
	done < "$f"
done

hth
EDIT:
Which then outputs as:
Code:
sh ccmbade.sh 
default :: name1 1111 chr start stop 
default :: 1 10 25 a t 
default :: 1 20 75 t - 
default :: 2 30 120 - a 
default :: 10 10 80 a g 
id handling
id :: 10 10 80 a g 
id handling
id :: 10 10 80 a g 
symbol handling
symbol :: 10 10 80 a g 
symbol handling
symbol :: 10 10 80 a g 
symbol handling
symbol :: 10 10 80 a g 
0 ~/tmp $

Last edited by sea; 01-11-2016 at 05:11 PM..
 

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